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STRs in panel
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Primary immunodeficiency

Gene: LAT

Green List (high evidence)

LAT (linker for activation of T-cells)
EnsemblGeneIds (GRCh38): ENSG00000213658
EnsemblGeneIds (GRCh37): ENSG00000213658
OMIM: 602354, Gene2Phenotype
LAT is in 6 panels

6 reviews

Eleanor Williams (Genomics England Curator)

Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 14 Oct 2020, 1:15 p.m. | Last Modified: 14 Oct 2020, 1:15 p.m.
Panel Version: 2.269
The following PubMed IDs were added to gene LAT (OMIM gene MIM#602354): 27522155. These publications have been associated with the gene by the immunodeficiencies subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208

Publications

Kimberly Gilmour (Great Ormond Street Hopsital)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Comment on list classification: Changed Amber to Green. After internal clinical review it was agreed that as there are two unrelated cases, two variants (frameshifting) and a supportive mouse model for T cell deficits plus a Green rating from external expert review this gene could be promoted to Green
Created: 11 Jul 2018, 4:09 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): LAT .PanelApp HGNC gene symbol check: LAT . IUIS Disease: LAT deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Nl to low, .IUIS Other affected cells: N/A. IUIS Associated features: Adenopathy, splenomegaly, recurrent infections, autoimmunity. IUIS Major category: Immunodeficiencies affecting cellular and humoral immunity. IUIS Subcategory: T-B+ Severe Combined Immune Deficiency (SCID)
Created: 2 Jul 2018, 10:35 a.m.
This gene was present in the original PanelApp PID panel dataset (review in April 2018) rated as Amber. The gene is absent from external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 10:30 a.m.

Rebecca Foulger (Genomics England curator)

Comment on list classification: 2 independent cases and 2 variants (a 2 bp deletion and a 1 bp insertion) reported in OMIM: 1 Arab family in Keller et al 2016/PMID:27242165, and 1 Pakistani family in Bacchelli et al 2017/PMID:27522155). No more current publications and not yet associated with a disease in DD-G2P. Therefore currently insufficient cases to rate green so rated as Amber and added 'watchlist' tag in anticipation of further publications.
Created: 29 Aug 2017, 9:31 a.m.
Added to this panel as advised by Helen Brittain after a new gene-disorder association was reported in OMIM in June 2017 (Immunodeficiency 52, MIM:617514).
Created: 29 Aug 2017, 9:26 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Immunodeficiency 52, 617514

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • SCID v1.6
  • Combined B and T cell defect v1.12
  • A- or hypo-gammaglobulinaemia v1.25
Phenotypes
  • Immunodeficiency 52, 617514
  • Adenopathy, splenomegaly, recurrent infections, autoimmunity
  • Immunodeficiencies affecting cellular and humoral immunity
OMIM
602354
Clinvar variants
Variants in LAT
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: lat has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to LAT. Publications for gene LAT were updated from 27522155; 27242165 to 27522155; 27242165 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to LAT.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to LAT.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to LAT.

12 Jul 2018, Gel status: 3

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

11 Jul 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: lat has been classified as Green List (High Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene LAT were set to Immunodeficiency 52, 617514, Adenopathy, splenomegaly, recurrent infections, autoimmunity, Immunodeficiencies affecting cellular and humoral immunity

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to LAT. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

SCID v1.6 was added to LAT. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Combined B and T cell defect v1.12 was added to LAT. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

LAT was added to Primary immunodeficiency disorders panel. Sources: Expert Review Amber, A- or hypo-gammaglobulinaemia v1.25

29 Mar 2018, Gel status: 2

Created

Louise Daugherty (Genomics England Curator)

LAT was created by Louise Daugherty